Microorganism mediated liquid fuels

ABSTRACT

A method for producing a liquid fuel from a hydrocarbon source. In one embodiment, the method comprises disintegrating a hydrocarbon source, treating the disintegrated hydrocarbon source, solubilizing the disintegrated hydrocarbon source, admixing a biochemical liquor, wherein the biochemical liquor comprises at least one conversion enzyme to form liquid hydrocarbons, separating liquid hydrocarbons, and enriching the liquid hydrocarbons to form a liquid hydrocarbon product. Further, the method comprises producing a liquid fuel in-situ. In certain embodiments the method comprises modified enzymes for producing the liquid fuels.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit under 35 U.S.C. §119(e) of U.S.Provisional Patent Application No. 61/141,552 filed Dec. 30, 2008 andU.S. Provisional Patent Application No. 61/146,816 filed Jan. 23, 2009the disclosures of which are hereby incorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

Not applicable.

BACKGROUND

1. Field of the Invention

This invention relates to producing liquid fuels, specifically toin-situ or ex-situ coal to liquid conversion.

2. Background of the Invention

Coals can also be converted into liquid fuels like gasoline or diesel byseveral different processes. In a developing commercial process, thecoal converted into a gas first, and then into a liquid, by using theFischer-Tropsch (FT) process. In the FT process, an indirect route, coalis first gasified to make syngas, a purified mixture of CO and H₂ gas.Next, FT catalysts are used to convert the syngas into lighthydrocarbons, like ethane, which are further processed into refinableliquid fuels. In addition to creating the fuels, syngas can also beconverted into methanol, which can be used as a fuel, or a fueladditive.

Alternatively, the coal may be converted directly to liquid fuels viahydrogenation processes. For example, the Bergius process, in which coalis liquefied by mixing it with hydrogen gas and heating the system.Several other direct liquefaction processes have been developed, such asthe Solvent Refined Coal (SRC) processes, which has spawned severalpilot plant facilities. Additionally, dried, pulverized coal mixed withroughly 1 wt % molybdenum catalysts may be hydrogenated by use of hightemperature and pressure synthesis gas produced. However, the syngasmust be produces in a separate gasifier.

However, these coal to liquid fuel processes involve the mining of thecoal from the ground. As is well documented, coal mining is a hazardousprocess, and many mines are forced into closure prior to the removal ofall usable products. Further, those mines that are operated safely leavebehind large columns of coal to support the ceiling and coal residues inthe mine walls. These sources of coal represent a significant amount ofenergy that is left abandoned by mining operations. Further, theseuntouched resources may be converted to liquid fuels for transportationpurposes. As such, there is a need in the industry for the removal ofabandoned, low quality, or residual coal from mining operations, for usein the coal to liquid production.

BRIEF SUMMARY

In one embodiment, a method for producing liquid hydrocarbon products,comprising, disintegrating a hydrocarbon source, treating thedisintegrated hydrocarbon source chemically, solubilizing thedisintegrated hydrocarbon source, admixing a biochemical liquor, whereinthe biochemical liquor comprises at least one enzyme to form liquidhydrocarbons, separating liquid hydrocarbons, and enriching the liquidhydrocarbons to form a liquid hydrocarbon product.

In another embodiment, a method for in-situ coal to liquid hydrocarbonconversion, comprising, locating an underground coal seam, drilling atleast one well, the well in contact the underground coal seam;pressurizing the underground coal seam with steam; cycling reactantsthrough the underground coal seam, wherein the reactants comprise atleast one enzyme, to form a slurry; withdrawing a portion of the slurry;processing the slurry, wherein the liquid hydrocarbon is separated fromthe slurry; and returning the slurry to the coal seam for furtherprocessing.

In further embodiments, a method for using an enzyme to produce liquidfuels, comprising selecting a microorganism, the microorganism producingan enzyme; modifying a microorganism genetically, to increase theproduction of the enzyme; modifying the enzyme structurally, to alterthe activity of the enzyme, to form a modified enzyme; collecting themodified enzyme to form a biochemical liquor comprising at least onemodified enzyme; and exposing a hydrocarbon source to the biochemicalliquor to form a liquid fuel precursor.

The foregoing has outlined rather broadly the features and technicaladvantages of the invention in order that the detailed description ofthe invention that follows may be better understood. The variouscharacteristics described above, as well as other features, will bereadily apparent to those skilled in the art upon reading the followingdetailed description of the preferred embodiments, and by referring tothe accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

For a detailed description of the preferred embodiments of theinvention, reference will now be made to the accompanying drawings ifvarious embodiments of the invention, in which:

FIG. 1 illustrates a general flow process schematic for converting coalto liquid.

FIG. 2 illustrates one embodiment of an ex-situ process for convertingcoal to liquid.

FIG. 3 illustrates one embodiment of an in-situ process for convertingcoal to liquid.

FIG. 4 illustrates a representative diagram of a catalytic antibody.

FIG. 5 illustrates a representative diagram of an activated catalyticantibody.

FIG. 6 illustrates a representative diagram of a wild type enzyme.

FIG. 7 illustrates a representative diagram of an activated enzymecomplex.

FIG. 8 illustrates a representative diagram of a directed evolution ofan activated enzyme complex.

FIG. 9 illustrates a representative diagram of site directed mutagenesisof an activated enzyme complex.

FIG. 10 illustrates a representative diagram of allosteric directedmutagenesis of an activated enzyme complex.

FIG. 11 illustrates a representative diagram of an active site redesignof an activated enzyme complex.

FIG. 12 illustrates a representative diagram of an active site rationaldesign of an activated enzyme complex.

FIG. 13 illustrates a representative diagram of a cofactor directedactive site redesign of an activated enzyme complex.

FIG. 14 illustrates a schematic of photofragmentation.

FIG. 15 illustrates a schematic of laser mediated photofragmentation.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

A process for converting coal to liquid fuels is disclosed. Coalcomprises any coal found or removed from a coal mine, seam, or pit. Thecoal may further comprise anthracite coals, or the coke from bituminouscoal. In certain instances, the coal comprises lignite, sub-bituminouscoal, other low-rank coals, and/or other hydrocarbon source, such as tarsands, without limitation. Alternatively, the coal comprises weathered,aged, leached, or degraded coal without limitation.

In certain instances, the coal is converted to liquid fuels by atwo-stage process. The process comprises ezymatically-catalyzedreactions. The first stage, Stage I, comprises the pretreatment andconversion of coal into liquid products by enzymes. In embodiments,Stage I converts coal feedstocks to liquid hydrocarbons. The feedstockscomprise coal remaining in coal mines, or in-situ feedstocks.Alternatively, the feedstocks comprise coal away from the coal mine, orex-situ feedstocks. In certain instances, the source of hydrocarbons maycomprise any source, such as tar sands, not preferred for otherindustries.

The second stage, Stage II, comprises the enrichment of the liquidhydrocarbon products. The enrichment, or improvement, of the liquidhydrocarbon product comprises further enzymatically-catalyzed reactions.Additionally, the reactions are enzyme-mediated processing steps. StageII further comprises the improvement of the liquid product propertiesfor use in fuels. The Stage II enzymatically-catalyzed processes changethe fuel performance. In exemplary instances, Stage II processing mayalter the cetane rating of diesel, or the octane rating of gasoline.

Compared to current processing techniques, the enzymatically-mediatedtwo-stage process requires less energy for processing. Additionally, thereaction conditions are milder, as the enzymes perform optimally inhomeostatic conditions of the microorganism producer. Further,additional enzymes or microorganisms may be implemented to sequestercontaminants regulated in liquid fuels. For instance, sulfur andnitrogen may be reduced or removed from the liquid fuels prior to finalproduct distillation. The early removal of polluting contaminants makesthe process adjustable to meet current and future emissions regulations.Additionally, the enzyme-mediated two-stage process is adaptable tofeedstocks previously inaccessible, for instance, coal columns in a minetoo dangerous for removal by retreat mining.

Microorganisms. In the disclosed process, microorganism-produced enzymesmediate the conversion. In embodiments, the microorganisms comprisebacteria, algae, or fungi. In certain instances, the microorganismscomprise heterotrophs that secrete enzymes for catalytic digestion ofhydrocarbons. The microorganisms use hydrocarbons as a carbon source forlife processes. The microorganisms are harvested from oil shales, oilsands, coal tar pits, or coal caves without limitation. For example, themicroorganisms may be derived from those found in the La Brea Tar Pits.Further, the microorganisms may be collected from geothermal springs,mud volcanoes, sulfur cauldrons, fumaroles, geysers, mudpots, or thelike, without limitation. The microorganisms may further compriseextremophiles, such as but not limited to hypoliths, endoliths,cryptoliths, acidophiles, alkaliphiles, thermophiles, ithoautotrophs,halophiles, or piezophiles. In exemplary embodiments, the microorganismscomprise archaebacteria. Alternatively, suitable microorganisms includethose found in the geneses Poria, Polyporus, Thiobacillus, Candida,Streptomyces, Psuedomonas, Penicillium, or Trichoderma. As understood byone skilled in the art, alternative microorganisms may be identifiedthat are suitable for application in the disclosed system, without beingnamed specifically, that do not vary in structure and functionsignificantly. Further, it can be envisioned that these microorganismsare envisioned as means to alter, improve, or modify the currentdisclosure.

In certain instances, the microorganisms are exposed to previously minedcoal, coal residues, or coal residues less favorable for powerproduction in order to harvest the enzymes. In instances, themicroorganism produces the enzymes naturally. As understood by oneskilled in the art, continued exposure to the substrate, such as coal,will lead to increased expression and production of the enzymes for theliquid hydrocarbon production.

Enzymes. The enzymes used in the disclosed process are obtained frommicroorganisms that produce these enzymes in high yields. In furtherembodiments, the microorganisms are genetically altered to produce theenzymes in high yields. Preferably, the enzymes are secretedextracellularly and/or release the enzymes into their environment.Alternatively, the cells are lysed and the enzymes are captured for usein coal processing. In embodiments, the enzymes are separated from themicroorganisms prior to use in the processing of coal. In order toreduce exposure, release, or environmental contamination, themicroorganisms are separated from the processing. No microorganisms aredirectly involved in any embodiments of the liquid fuel productionprocess. Furthermore, the facilities used to grow these organisms havesufficient provisions to isolate host organisms from the naturalenvironment.

Alternatively, the microorganisms undergo site-directed mutagenesis toup-regulate, over-express, and/or increase, the production of enzymes.Site directed mutagenesis comprises the mutation of a DNA molecule atspecific nucleic-acid base-pair sequence. Site directed mutagenesis mayoccur in the chromosomal DNA, or in extra-chromosomal DNA, from avector. Additionally, the site-directed mutagenesis may comprise genedeletion/excision, primer mediated mutagenesis, cassette mutagenesis,add-on mutagenesis, mismatch mutagenesis, gene conversion, topologicalmanipulation, specialized recombination, or PCR-mediated mutagenesis.Further, mutagenesis and over-expression of a gene may be induced by anymutagen. For instance, ionizing radiation, UV exposure, deamination,intercalation, alkylation, analog insertion, transposon multiplication,and other molecular biology techniques may be used, without limitation.In certain instances, mutagen exposure induces the microorganism toacquire a vector, such as a plasmid. Further, mutagenesis may induce theincorporation of vector DNA into the chromosomal DNA. For the purpose ofthis disclosure, directed, mutagenic technique may be implemented inorder to induce additional production of an enzyme. Further, themutagenesis may be used to increase the activity of the enzyme.

In certain instances, the enzymes are chemically modified afterproduction. The enzymes may be modified prior to or after harvestingfrom the microorganisms. Any process known to one skilled in the art maybe implemented, such as but not limited to addition of functionalgroups, addition of other peptides, altering the chemical nature, and/orstructural changes. For example, processes like acylation,glycosylation, ubiquitination, deamidation, and/or cleavage, areenvisioned to have applications within the present disclosure, withoutlimitation.

The produces and modified enzymes are utilized in biochemical liquor.The biochemical liquor comprises a liquid mixture of proteins, enzymes,inorganic catalysts, and organic and inorganic compounds. Thebiochemical liquor further comprises salts, electrolytes, metals, and/orother molecules that aid, improve, or alter the operations of an enzymebroth, or biochemical liquor. The biochemical liquor is a mixture of atleast one of each of the aforementioned groups without limitation. Thebiochemical broth may be suspended in any known solvent; preferablyorganic solvents. In exemplary embodiments, water is the solvent.

Process. As illustrated in FIG. 1, the process comprises a flow of coalthrough a sequence of individual treatment steps. In STAGE I, theprocess comprises at least one pretreatment step. The coal thenundergoes solubilization, which may be included in the pretreatmentsteps. The pretreated, solubilized coal material is converted to liquidhydrocarbons. Simultaneously, or sequentially, the material may undergosulfur and nitrogen conversion. Removing sulfur and nitrogen from theproduct improves performance of the fuel after processing, such asseparation. The different fuels are separated, such that aqueous phasereactants are recycled, and/or the wastewater is treated for return tothe system. In STAGE II, the hydrocarbon phase products from theconversion step are further refined. The refining of the productscomprises fuel refining, enrichment, and distillation to improve productqualities.

Pretreatment. The pretreatment step comprises a physical and chemicaldegradation of the coal, to produce a degraded coal. In order toincrease efficiency of the disclosed process it is advantageous toincrease the surface area of the material. The surface area of the coalmay be increased by reducing the particle volume, such as in the processof comminution. For instance, surface coal, mined coal, coal tailings,or remaindered coal is mechanically broken down or crushed into a fineparticulate. Remaindered coal may comprise, without limitation, coalsourced from any industry from which it was rejected for use. Theparticulate may comprise pebbles, dusts, powders, or the like withoutlimitation.

In certain instances, the coal is treated in-situ, for instance, in anunderground coal seam, by high-pressure steam. Underground wells,conduits, and/or other lines deliver steam to a coal mine. The steam maybe pressurized, superheated, or combinations thereof in order toincrease penetration into the seam. The steam is used to fracture thecoal bed underground prior to pretreatment. Further, the high-pressuresteam mechanically separates the coal from surrounding rock formations.

Additionally, the coal is subjected to a chemical treatment. Chemicaltreatment of the coal increases the reactivity of the coal.Additionally, chemical treatment is designed to remove, digest, oreliminate non-coal materials from the coal products. Further, thechemical treatment may increase the surface area of the coal further byinducing the formation of pores, cavities, pits, and the like. Thechemical treatment may compromise an oxidative agent. In certainembodiments, mild ionic, acid, base, or free radical solutions areapplied to oxidize the coal. In an embodiment, the solution comprises amild acid solution. In an exemplary embodiment, the chemical treatmentcomprises hydrogen peroxide. The hydrogen peroxide is in concentrationsbetween about 10% and about 50%; alternatively between about 20% andabout 40%, and in preferably about 30% hydrogen peroxide. As discussedabove, the solutions are injected into coal mines with steam, or water,therefore it is preferable the solutions are aqueous. In certaininstances, an inorganic chemical treatment may be implemented.

Solubilization. Further, the pretreatment steps comprise solubilizationof the degraded coal. Once mechanically disintegrated, and chemicallyoxidized, a first set of enzymes is introduced to break thecross-linking bonds in coal. In certain instances, the first enzymes maybe derived from enzymes found, for example, in the genera Peoria,Polypore's, genuses Poria, Polyporus, without limitation. The firstenzymes allow the coal particles to dissolve into the liquid medium. Inembodiments, the liquid medium is the same as is used to deliver theenzymes. In certain instances, the medium is the biochemical liquordescribed above. Further, the liquid medium comprises an aqueous medium.The solubilized coal particles are suspended in the liquid mediumforming a coal slurry; alternatively, a coal suspension, a coal mixture,a coal colloid, or a coal solution, without limitation. The coal slurryimproves accessibility to the coal particles by the enzymes from thebiochemical liquor. Suspending the particles in the medium may improvereaction kinetics during the subsequent enzymatically mediated steps.The coal slurry further improves transfer of the coal between processingsteps.

Conversion. After solubilization, the coal is processed by conversionsteps. In certain instances, the solubilized coal in the coal slurry isconverted to smaller or lower hydrocarbons. The lower hydrocarbons maycomprise any hydrocarbon, for instance hydrocarbons comprising betweenabout 24 carbons and about 2 carbons. The second enzyme, or secondenzyme solution, is maintained in the biochemical broth. The secondenzyme solution may be derived from enzymes produced by microorganismsfor the genera, Thiobacillus, Candida, Streptomyces, Psuedomonas,Penicillium, Trichoderma, for example, without limitation. The secondenzyme may be introduced to the coal slurry during the conversionprocess. In certain instances, the exposure of the coal slurry to asecond enzyme comprises converting coal to lower molecular weighthydrocarbon fractions. Alternatively, the second enzyme is a convertingenzyme. Converting enzymes are those selected, engineered, or modifiedto catalytically convert large hydrocarbon molecules found in coal tolower molecular weight hydrocarbons. During the conversion step, thehydrocarbons undergo saturation, and sulfur, nitrogen, and othercontaminant conversion. The conversion step forms a reaction slurry, ora hydrocarbon slurry with the biochemical liquor.

The enzymatic conversion reactions successively break the native,original, or solubilized, coal particles into smaller hydrocarbonmolecules that remain in the reaction slurry. The enzymatic conversionreactions convert the high molecular weight molecular components of coalto lower molecular weight mixtures of hydrocarbon liquids andhydrocarbon gases.

During conversion, certain waste products, contaminants, and potentialpollutants are removed from the process. In certain instances, theremoval of these products is mediated by a third enzyme added to thereaction slurry. The third enzyme, or third enzyme solution, reacts withthe products of catalytic conversion to liberate sulfur from thehydrocarbon complexes and form a variety of simpler sulfur-containingcompounds, which are soluble in the reaction slurry. The solublesulfur-containing compounds may be filtered from the reaction slurry andprocessed for other products.

Additionally, in order to remove other waste products, contaminants, andpotential pollutants, a fourth enzyme may be added to the reactionslurry. In certain instances, any number of waste removal enzymes may beused to specifically eliminate, sequester, or cleave the unwantedcompounds. In certain embodiments, the fourth enzyme solution reactswith the products of catalytic conversion to liberate nitrogen and forma variety of simpler nitrogen-containing compounds, which are soluble inreaction slurry.

The processed wastes may comprise gases solubilized in the reactionslurry. Gases may comprise nitrogen, oxides of nitrogen, sulfur, oxidesof sulfur, carbon monoxide, carbon dioxide, and other gases withoutlimitation. Certain waste products are used for further processes, suchas syngas production, or catalyzed synthesis of liquid fuels. Further,enzymatically-catalyzed reactions convert the complex sulfur andnitrogen compounds found in coal to simpler forms that are removedduring product separation.

As understood by one skilled in the art, the reaction properties such astemperature, pressure, pH and residence time are differentiallymonitored, and controlled for maximized production. In certaininstances, the reaction properties are controlled to obtain adistribution of hydrocarbon molecular weights in the product stream.Further, as the reaction slurry comprises the biochemical liquor,altering the conditions may optimize conversion.

As discussed hereinabove, the biochemical liquor comprises any number ofenzymes. As understood by one skilled in the art, each enzyme haspreferred conditions for efficient catalysis. As such, cycling thereaction conditions, such as temperature and pressure, is envisioned tomaximize the efficiency of any portion of the process, or the action ofany portion of the enzymes. In other embodiments, the conversion stepconsists of separate reaction vessels for the solubilization, catalyticcracking, and nitrogen and sulfur conversion reactions. Such anarrangement permits different operating conditions to be used in eachvessel, such as temperature and individual reactor recycle rates, tooptimize the enzyme-catalyzed reactions.

Product Separation. Following conversion, the hydrocarbon mixture issent into settling tanks. In embodiments, the settling tank may be anyvessel configured for separating the hydrocarbon liquid from the aqueouscoal slurry. In certain instances, the settling tank may comprise adynamic settler, wherein a constant low volume, or slow velocity, streamof the reaction slurry is introduced to separate the aqueous andhydrocarbon phases. Alternatively, the settling tank comprises a staticsettler, where the aqueous phase coal slurry settles from the lighterhydrocarbons by virtue of gravity. In certain embodiments, the remainingsulfur and nitrogen compounds distribute to the water phase. Thehydrocarbon phase is separated by drawing off the lighter hydrocarbonlayer from the denser aqueous layer. Alternatively, a conduit withdrawsthe aqueous phase from the bottom of the tank.

Product Enrichment. The hydrocarbon layer, which already containsgasoline, kerosene, diesel, and fuel oils is sent to Stage II where itis further upgraded by converting the lower-valued fractions, naphtha,diesel, fuel oils, waxes, and the like to higher-valued fractions suchas gasoline or kerosene. In embodiments, the product enrichment maycomprise enzymatic conversion, molecular photofragmentation, conversion,and enzyme assisted molecular photo-fragmentation conversion. In certaininstances, the product enrichment comprises a fifth enzyme, or fifthenzyme solution introduced to the hydrocarbon products from theseparation step. Following enrichment, the hydrocarbon mixture isseparated into final products by conventional distillation.

Ex-situ Processing. FIG. 2 illustrates an embodiment of processing ofex-situ coal feedstocks continuously, or an EX-system 10. In theEX-system 10, pretreatment, conversion, and product processes aredesigned to be in fluid communication. In EX-system 10, the coal isfirst ground into small particles by mechanical means 12. As previouslydescribed, the mechanical means 12 creates a particulate product stream14. The particulate product stream is introduced to chemical treatmentsystem 16, comprising, for example, a weak acid solution. In certaininstances, mechanical means 12 and chemical treatment system 16 maycomprise a single vessel, or single processing facility. The coal andacid solution form coal slurry where the coal undergoes pre-oxidation.The extent of the pre-oxidation is determined by the residence time ofthe slurry in the chemical treatment system 16. Further, in combinedembodiments, the oxidation of the coal in the coal slurry may becontrolled, at least in part, by the degree of agitation provided bymixers 18.

The slurry product stream 20 is then pumped out of the feed tank andinto a reactor stage 22. The reactor stage 22 comprises thesolubilization reaction. In certain instances, the first enzyme stream24, with enzymes selected for solubilizing the coal, is injected intoslurry product stream 20. Alternatively, first enzyme stream 24 isinjected directly into reactor stage 22. Without wishing to be limitedby theory, it may be beneficial for first enzyme stream 24 to beintroduced to slurry stream 20 prior to introduction to reactor stage22.

Reactor stage 22 comprises the enzyme mediated catalytic conversionreaction. Second enzyme stream 26 is injected into reactor stage 22. Theenzymes react catalytically, convert the large hydrocarbon molecules,and produce product stream 30. Further, third enzyme stream 27 toconvert sulfur compounds and fourth enzyme stream 28 to convert thenitrogen compounds are added to reactor stage 22. The third enzymestream 27 and fourth enzyme stream 28 convert the respectivecontaminants found in the coal slurry 20 into simpler, water-solubleforms. Reactor stage effluent 23 is continuously split between a recyclestream 25, which is pumped back into the reactor stage 22, and a productstream 30.

In other embodiments, the reaction stage 22 consists of separatereaction vessels for the solubilization, catalytic conversion, andnitrogen and sulfur conversion reactions. A multiple reactor arrangementpermits different operating conditions to be used in each vessel, suchas temperature and individual reactor recycle rates, to optimize thedifferent suites of reactions.

The product stream 30 is pumped into the separation stage 32. Separationstage 32 may comprise gas vent 33 for withdrawing the gases and volatilecompounds released during separation. In certain instances, gas vent 33vents some gases that were dissolved in product stream 30. Theseparation stage 32 comprises the step where the aqueous phase 36settles out under the hydrocarbon phase 34. Separation stage 32comprises a settler, or settling vessel. Alternatively, separation stageis a filter or other apparatus to separate aqueous and hydrocarbonphases from product stream 30. Separation stage 32 comprises acontinuous flow, oil separation vessel. The aqueous phase 36 iswithdrawn from separation stage 32 and routed via recycle stream 39 tothe reactor stage 22. The recycle stream comprises a wastewatertreatment system. The treatment system comprises any system configuredas a sour water treatment, configured to remove residuum, as well asnitrogen and sulfur by-products. Treated water is then recycled back tothe reactor section.

In certain instances, the hydrocarbon phase 34 may be withdrawn from thetop of the settler as hydrocarbon stream 38 for enrichment and/ordistillation to produce transportation fuels. The hydrocarbon stream 38is pumped to a product enrichment stage.

In-Situ Processing Another embodiment involves the continuous processingof in-situ coal, or IN-system 100, which is illustrated in FIG. 3. Inthis embodiment, the IN-system 100 comprises an abandoned, collapsed,inaccessible, or otherwise difficult to mine coal deposit, orunderground coal seam 101. In embodiments, at least one well 102 isdrilled into the coal seam 101. The wells 102 are generally configuredfor the transport of liquids and slurries between the underground coalseam 101 and the processing center 120. Further, the wells 102 may beconfigured for the continuous circulation of process fluids in and outof the underground coal seam 101. It can be envisioned that a pluralityof wells 102 would improve product yield, processing time, and thegeneral economics of the IN-system 101, without limitation.

The IN-system 100 process begins with the injection of steam in the well102 conduits to induce fracturing of the underground coal seam 101. Thisfracturing step 105 is configured to break the coal seam intoparticulates, coal gravel, or the like. In certain instances, usinghigh-pressure steam is according to conventional practices of theunderground coal mining industry.

After the fracturing step 105 is complete, the high-pressure steam iswithdrawn. The oxidation step 106 comprises injecting an acid solutionto pre-oxidize the fractured coal. In embodiments, the acid solution isrecycled continuously to form a circulating process stream 150, suchthat the acid is pumped into well 102A at one side of the seam, pumpedout of well 102B on the other side of the seam. To complete the cycle,the acid solution is transported back and pumped into the first well102A. The circulating process stream 150 may be repeated until thedesired level of pre-oxidation is achieved.

As described above, the solubilization step 107 may comprise theintroduction of the first enzyme solution into the underground coal seam101. The first enzyme solution is introduced into the circulatingprocess stream 150 to solubilize the exposed coal into the circulatingprocess solution.

Once an adequate level of soluble coal is achieved, to create coalslurry in the circulating process stream 150, the additional enzymes areadded either sequentially or simultaneously. In certain instances, thesecond enzyme 106, third enzyme 107, and fourth enzyme 108 solutions areadded to the circulating stream 150. As described herein above, thesecond enzyme stream 106 is selected to catalytically crack thehydrocarbons. The third enzyme 107 and fourth enzyme 108 solutions areselected to remove sulfur and nitrogen-containing compounds and/or wasteproducts from the circulating process stream 150. In embodiments,further enzyme streams may be injected into circulating process stream150 to optimize the solubilization and conversion of the coal.

A portion of the circulating process stream 150 is then split and takenas a raw product stream 160 and sent to a processing stage 120. Theprocessing stage 120 is similar to the one used in ex-situ embodimentsof the process described above. Separation vessel 162 comprises the stepwhere the aqueous phase 163 settles out under the hydrocarbon phase 164.Separation vessel 162 comprises a settler or settling vessel. Theaqueous phase 163 is withdrawn from separation vessel 162 and routed viarecycle stream 170 to the circulating process stream 150. The recyclestream 170 comprises a wastewater treatment system. The treatment systemcomprises any system configured for sour water treatment, configured toremove residuum, as well as nitrogen and sulfur by-products. In certaininstances, the hydrocarbon phase 164 may be withdrawn from the top ofthe settler as hydrocarbon stream 168 for enrichment and/or distillationto produce transportation fuels. The hydrocarbon stream 38 is pumped toa product enrichment stage.

Mutagenesis. Methods used to produce suitable enzymes for implementationin Stage II for fuel upgrade include using catalytic antibodies. Asillustrated in FIG. 4, biological enzymes are identified for thecatalytic processes desired. In certain instances, the biologicalenzymes are derived from the microorganisms discussed herein above. Infurther embodiments, the enzymes comprise Mother Nature only (MNO)enzymes. MNO enzymes are the phenotypic expressions of unmodifiedgenetic sequences within the microorganisms. Alternatively, MNO enzymesare wild-type enzymes. In further instances, illustrated in FIG. 5, theMNO enzymes are selected from those that comprise an activated enzyme.In certain instances, the activated enzyme screening is conducted by anantibody assay. Alternatively, any suitable screening method maycomprise any suitable protocol to identify the wild type MNO enzymes, asfurther illustrated in FIGS. 6 and 7.

The MNOs selected are formed by directed evolution, as illustrated inFIG. 8. The selected MNOs are subject to site-directed and randommutagenesis throughout the enzyme, not solely restricted to the activesite. In certain instances, the enzymes are also subject to mutagenesisat allosteric sites, and at sites remote from active and/or allostericsites. The mutagenesis at multiple sites comprises a means to bothpromote and restrict potential products as illustrated in FIGS. 9 and10. In certain instances, the mutagenesis includes active site chemicalredesign as shown in FIG. 11. Preferably, the results include a rationaldesign enzyme, or enzymatic structure.

The structure is synthesized, computationally designed, with motifsattached to enzyme scaffolds. As enzymes are rather large molecules,having hundreds of amino acids, tens of kilo Daltons (Kds), andthousands of cubic angstroms, they may be considered spatiallyinefficient. In certain instance, large enzyme molecules comprise smallactive sites. Enzymatic reactive sites are quite small by comparison andthe other folded amino acids serve as a scaffolding to create thereactive site volume. These “other” amino acids can be, relativelyspeaking, quite far from the active site of the enzyme as illustrated inFIG. 12. Additionally, the enzymes may include cofactor attachment siteredesigns, shown in FIG. 13. In order to induce cofactor attachment siteredesigns the implementation of site directed mutagenesis are repeatedas discussed hereinabove, for example, paragraph 21.

As diagrammed in FIG. 14, a shaped IR femtosecond laser pulse may beimpinged upon the enzymatic complex to induce reactant fragmentation.Further, it can be envisioned that any particular impingent radiation,known to one skilled in the art, may be capable of the same reactantfragmentation, without limitation. The laser pulse for directedfragmentation of reactants/conversion to products may aid the formationof reactant products. As understood by one skilled in the art, multiplefragmentation reactant products may be formed. In certain instances, themultiple fragmentation products may be advantageous for the formation ofa range of reactant fragments. Alternatively, the shaped IR femtosecondlaser pulses in conjunction with above mentioned enzyme techniques toassist in selective fragmentation of reactants at enzymatic activesites, allosteric sites, and sites remote from binding or allostericsites as shown in FIG. 15. As understood by one skilled in the art, thebonding of the reactant, hydrocarbon, molecular to the enzyme reactivesite may comprise a covalent, non-covalent, hydrogen, ionic, Van derWaals, or other bond, interaction, coupling, or association, withoutlimitation. Further, the enzyme reactive site is configured to restrictthe reactant molecule, and its range of movement. Further, the reactivesite restricts internal degrees of freedom, to favorably target thefemtosecond laser pulses to the preselected internal bond. In certaininstances, the enzyme reactive site damps the internal degrees offreedom, such that internal vibrational rearrangement (IVR) isprevented, and the laser energy is focused to the preselected internalbond.

While the preferred embodiments of the invention have been shown anddescribed, modifications thereof can be made by one skilled in the artwithout departing from the spirit and teachings of the invention. Theembodiments described and the examples provided herein are exemplaryonly, and are not intended to be limiting. Many variations andmodifications of the invention disclosed herein are possible and arewithin the scope of the invention. Accordingly, the scope of protectionis not limited by the description set out above, but is only limited bythe claims that follow, the scope including all equivalents of thesubject matter of the claims.

1. A method for producing liquid hydrocarbon product comprising,disintegrating a hydrocarbon source; treating the disintegratedhydrocarbon source chemically; solubilizing the disintegratedhydrocarbon source to form a slurry; admixing a biochemical liquor intothe slurry, wherein the biochemical liquor comprises at least oneconversion enzyme, to form liquid hydrocarbons; separating liquidhydrocarbons from the slurry, wherein contaminants remain in the slurry;and enriching the liquid hydrocarbons to form a liquid hydrocarbonproduct.
 2. The method of claim 1, wherein disintegrating thehydrocarbon source comprises comminution of the hydrocarbon source. 3.The method of claim 2, wherein comminution comprises grinding.
 4. Themethod of claim 2, wherein comminution comprises high-pressure steamtreatment.
 5. The method of claim 1, wherein treating the disintegratedhydrocarbon source further comprises oxidation of the hydrocarbonsource.
 6. The method of claim 1, wherein solubilizing the disintegratedhydrocarbon source comprises treating the disintegrated hydrocarbonsource with at least one enzyme.
 7. The method of claim 1, whereinadmixing biochemical liquor comprises admixing at least one additionalenzyme.
 8. The method of claim 7, wherein admixing at least oneadditional enzyme further comprises admixing an enzyme for converting ahydrocarbon source to lower molecular weight hydrocarbons.
 9. The methodof claim 1, wherein separating liquid hydrocarbons comprises a processof settling the slurry from the liquid hydrocarbon.
 10. The method ofclaim 1, wherein separating liquid hydrocarbons comprises settlingcontaminants from the liquid hydrocarbon.
 11. The method of claim 1,wherein enriching the liquid hydrocarbon comprises admixing the liquidhydrocarbon with at least one enzyme.
 12. The method of claim 1, whereinthe hydrocarbon source comprises at least one selected from the groupconsisting of coal, anthracite coal, bituminous coal, lignite,sub-bituminous coal, low-rank coals, coke, tar sand, oil shale, andcombinations thereof.
 13. The method of claim 1, wherein the biochemicalliquor comprises a modified enzyme.
 14. The method of claim 13, whereinthe modified enzyme comprises an enzyme that is genetically modified.15. The method of claim 13, wherein the modified enzyme comprises anenzyme that is chemically modified.
 16. The method of claim 13, whereinthe modified enzyme comprises an enzyme configured for bond selectivephoto-fragmentation.
 17. The method of claim 1, wherein the method isconducted in-situ in a coal mine.
 18. The method of claim 1, wherein themethod is conducted ex-situ on mined coal.
 19. The method of claim 1,wherein enriching the liquid hydrocarbons comprises improving the liquidhydrocarbon product qualities prior to distillation.
 20. The method ofclaim 1, wherein the liquid hydrocarbon product comprises at least oneselected from the group consisting of gasoline, diesel, kerosene, anddistillates thereof.
 21. A method for in-situ coal to liquid hydrocarbonconversion, comprising: locating an underground coal seam; drilling atleast one well, the well in contact with the underground coal seam andhaving a means to cycle liquids therethrough; pressurizing theunderground coal seam with steam; cycling reactants through theunderground coal seam, wherein the reactants comprise at least oneenzyme, to form a slurry; withdrawing a portion of the slurry;processing the slurry to produce the liquid hydrocarbon; separating theliquid hydrocarbon from the slurry; and returning the slurry to the coalseam for further processing.
 22. The method of claim 21, wherein the atleast one well is in fluid communication with a reactant stream.
 23. Themethod of claim 21, wherein the at least one well is in fluidcommunication with a slurry processing stream.
 24. The method of claim21, wherein cycling reactants to form a slurry further comprisessolubilizing the coal to form a slurry; converting the coal to formliquid hydrocarbons; separating contaminant compounds from the liquidhydrocarbons, wherein the contaminant compounds comprise pollutants;settling the slurry from the liquid hydrocarbons, wherein the liquidhydrocarbons are suitable for liquid fuels; and processing the liquidhydrocarbons to liquid fuels.
 25. The method of claim 24, wherein thestep of solubilizing the coal comprises treating the coal with at leastone enzyme.
 26. The method of claim 24, wherein the step of convertingthe coal comprises treating the coal with at least one enzyme.
 27. Themethod of claim 24, wherein the step of separating contaminant compoundscomprises treating the liquid hydrocarbons with at least one enzyme. 28.A method for using an enzyme to produce liquid fuels, comprisingselecting a microorganism, the microorganism producing an enzyme;modifying a microorganism genetically, to increase the production of theenzyme; modifying the enzyme structurally, to alter the activity of theenzyme, to form a modified enzyme; collecting the modified enzyme, toform a biochemical liquor comprising at least one modified enzyme; andexposing a hydrocarbon source to the biochemical liquor to form a liquidfuel precursor.
 29. The method of claim 28, wherein the step ofselecting a microorganism comprises selecting at least one microorganismchosen from the group consisting of hypoliths, endoliths, cryptoliths,acidophiles, alkaliphiles, thermophiles, ithoautotrophs, halophiles,piezophiles, and combinations thereof.
 30. The method of claim 28, wheremodifying a microorganism comprises inserting a nucleic acid vector. 31.The method of claim 28, wherein modifying a microorganism geneticallycomprises directed mutagenesis.
 32. The method of claim 28, whereinmodifying an enzyme comprises structurally changing an enzyme.
 33. Themethod of claim 28, wherein exposing the biochemical liquor to thehydrocarbon source further comprises transmitted-radiation directedfragmentation.